Nix nits

[SinervaDev]

The Nix(OS) packaging seems to work just fine, and there were no major issues in the code or documentation. This PR fixes the following smaller problems to further ReFine the packaging:

1. Deduplicated dev shell
2. Deduplicated /etc/pkcs11/modules/refineid.module
3. Removed the claim that flakes are on by default on recent installs.
4. Added NIX_CONFIG prefix to 1b's rebuild command
5. Added inputs.nixpkgs.follows = "nixpkgs" to the refineid input in the example
6. Updated nix profile install to the new nix profile add
7. Added (not recommended) to the fresh machine section
8. Formatted Nix code (in code and docs)

I hope you will accept my humble contribution to your project 🙇‍♂️

LLM Disclosure

The code and documentation were reviewed and ReFined by a private LLM that has been in continuous training for 25 years. The model will not be made available for public use.